Starting phenix.real_space_refine on Wed Sep 17 07:04:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zab_39877/09_2025/8zab_39877.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zab_39877/09_2025/8zab_39877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zab_39877/09_2025/8zab_39877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zab_39877/09_2025/8zab_39877.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zab_39877/09_2025/8zab_39877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zab_39877/09_2025/8zab_39877.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4098 2.51 5 N 1127 2.21 5 O 1234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6497 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1576 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 8, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1600 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1685 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1636 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 197} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 1.68, per 1000 atoms: 0.26 Number of scatterers: 6497 At special positions: 0 Unit cell: (86.184, 151.899, 93.7251, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1234 8.00 N 1127 7.00 C 4098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 191 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 191 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 255.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 18 sheets defined 6.5% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 57 through 60 removed outlier: 3.522A pdb=" N GLN C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 71 through 78 removed outlier: 4.383A pdb=" N GLY C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA C 77 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 213 Processing helix chain 'D' and resid 210 through 213 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.537A pdb=" N ARG E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 209 through 213 removed outlier: 3.774A pdb=" N MET E 213 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 209 through 213 removed outlier: 3.507A pdb=" N PHE G 212 " --> pdb=" O PRO G 209 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET G 213 " --> pdb=" O GLU G 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 209 through 213' Processing sheet with id=AA1, first strand: chain 'C' and resid 11 through 14 removed outlier: 5.833A pdb=" N ILE C 11 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA C 115 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 13 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 36 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.667A pdb=" N ALA C 177 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 179 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 181 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 133 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR C 140 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 175 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.667A pdb=" N ALA C 177 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 179 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 181 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 133 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR C 128 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS C 134 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 123 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 147 through 151 removed outlier: 3.692A pdb=" N LEU C 200 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL D 123 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER C 205 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL D 125 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER C 207 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY D 127 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 134 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR D 173 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 151 removed outlier: 3.692A pdb=" N LEU C 200 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL D 123 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER C 205 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL D 125 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER C 207 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY D 127 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 134 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR D 173 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 166 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.685A pdb=" N ALA D 81 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.093A pdb=" N ILE D 11 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA D 115 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA D 13 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU D 36 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL D 49 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP D 38 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 147 through 151 removed outlier: 3.667A pdb=" N THR D 192 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 193 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.719A pdb=" N SER E 104 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 93 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL E 49 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS E 51 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG E 54 " --> pdb=" O LYS E 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 122 through 128 removed outlier: 3.515A pdb=" N LEU E 122 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG E 134 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ARG E 134 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE E 181 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU E 136 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL E 179 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE E 138 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR E 177 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG E 140 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL E 175 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET E 174 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS E 162 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.531A pdb=" N LYS E 202 " --> pdb=" O ILE E 193 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN E 200 " --> pdb=" O ASN E 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.295A pdb=" N ILE G 11 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ALA G 115 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA G 13 " --> pdb=" O ALA G 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.668A pdb=" N LEU G 21 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 82 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS G 23 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 80 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA G 81 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 48 through 52 removed outlier: 3.504A pdb=" N PHE G 48 " --> pdb=" O TRP G 38 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET G 34 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU G 35 " --> pdb=" O GLN G 100 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN G 100 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 122 through 129 removed outlier: 5.816A pdb=" N ILE G 123 " --> pdb=" O ILE G 138 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE G 138 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET G 125 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU G 136 " --> pdb=" O MET G 125 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY G 127 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS G 162 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 147 through 151 213 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2159 1.34 - 1.46: 1484 1.46 - 1.58: 2928 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 6633 Sorted by residual: bond pdb=" CB PRO C 10 " pdb=" CG PRO C 10 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.93e+00 bond pdb=" CB PRO D 159 " pdb=" CG PRO D 159 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.63e+00 bond pdb=" CB PRO C 159 " pdb=" CG PRO C 159 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.02e+00 bond pdb=" CB ASP G 130 " pdb=" CG ASP G 130 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.84e+00 bond pdb=" CB ARG G 103 " pdb=" CG ARG G 103 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.36e+00 ... (remaining 6628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 8899 3.12 - 6.23: 75 6.23 - 9.35: 9 9.35 - 12.46: 2 12.46 - 15.58: 2 Bond angle restraints: 8987 Sorted by residual: angle pdb=" CA PRO C 10 " pdb=" N PRO C 10 " pdb=" CD PRO C 10 " ideal model delta sigma weight residual 112.00 99.21 12.79 1.40e+00 5.10e-01 8.35e+01 angle pdb=" CA PRO D 159 " pdb=" N PRO D 159 " pdb=" CD PRO D 159 " ideal model delta sigma weight residual 112.00 99.62 12.38 1.40e+00 5.10e-01 7.82e+01 angle pdb=" C LEU D 43 " pdb=" N ARG D 44 " pdb=" CA ARG D 44 " ideal model delta sigma weight residual 121.70 137.28 -15.58 1.80e+00 3.09e-01 7.49e+01 angle pdb=" C LEU C 43 " pdb=" N ARG C 44 " pdb=" CA ARG C 44 " ideal model delta sigma weight residual 121.70 132.89 -11.19 1.80e+00 3.09e-01 3.86e+01 angle pdb=" N PRO C 10 " pdb=" CD PRO C 10 " pdb=" CG PRO C 10 " ideal model delta sigma weight residual 103.20 95.00 8.20 1.50e+00 4.44e-01 2.99e+01 ... (remaining 8982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 3368 16.95 - 33.91: 477 33.91 - 50.86: 132 50.86 - 67.81: 26 67.81 - 84.76: 2 Dihedral angle restraints: 4005 sinusoidal: 1597 harmonic: 2408 Sorted by residual: dihedral pdb=" CA PHE D 26 " pdb=" C PHE D 26 " pdb=" N PRO D 27 " pdb=" CA PRO D 27 " ideal model delta harmonic sigma weight residual 180.00 134.92 45.08 0 5.00e+00 4.00e-02 8.13e+01 dihedral pdb=" CB CYS D 137 " pdb=" SG CYS D 137 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -131.08 45.08 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS E 137 " pdb=" SG CYS E 137 " pdb=" SG CYS E 191 " pdb=" CB CYS E 191 " ideal model delta sinusoidal sigma weight residual -86.00 -125.87 39.87 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 4002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 671 0.039 - 0.078: 214 0.078 - 0.118: 104 0.118 - 0.157: 8 0.157 - 0.196: 1 Chirality restraints: 998 Sorted by residual: chirality pdb=" CA PRO D 159 " pdb=" N PRO D 159 " pdb=" C PRO D 159 " pdb=" CB PRO D 159 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA PRO C 10 " pdb=" N PRO C 10 " pdb=" C PRO C 10 " pdb=" CB PRO C 10 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE E 3 " pdb=" N ILE E 3 " pdb=" C ILE E 3 " pdb=" CB ILE E 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 995 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 158 " -0.090 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO D 159 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO D 159 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 159 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 9 " 0.078 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO C 10 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 10 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 10 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 158 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO C 159 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 159 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 159 " -0.056 5.00e-02 4.00e+02 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 377 2.72 - 3.27: 6265 3.27 - 3.81: 10125 3.81 - 4.36: 11817 4.36 - 4.90: 20603 Nonbonded interactions: 49187 Sorted by model distance: nonbonded pdb=" OD1 ASP G 183 " pdb=" N LYS G 184 " model vdw 2.176 3.120 nonbonded pdb=" N GLN C 100 " pdb=" OE1 GLN C 100 " model vdw 2.201 3.120 nonbonded pdb=" NH1 ARG E 67 " pdb=" OE2 GLU E 91 " model vdw 2.225 3.120 nonbonded pdb=" O VAL D 46 " pdb=" OG SER D 61 " model vdw 2.240 3.040 nonbonded pdb=" N GLU E 58 " pdb=" OE1 GLU E 58 " model vdw 2.248 3.120 ... (remaining 49182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 through 213)) selection = (chain 'D' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 183 or resid 188 through 202 or \ (resid 203 through 204 and (name N or name CA or name C or name O or name CB )) \ or resid 205 through 213)) } ncs_group { reference = (chain 'E' and (resid 5 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 103 or (resid 104 and (name N or na \ me CA or name C or name O or name CB )) or resid 105 through 106 or (resid 107 t \ hrough 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 151 or (resid 152 and (name N or name CA or name C or name O or name CB \ )) or resid 153 through 214)) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 6641 Z= 0.173 Angle : 0.796 15.579 9003 Z= 0.444 Chirality : 0.046 0.196 998 Planarity : 0.008 0.127 1167 Dihedral : 16.465 84.762 2443 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.46 % Favored : 93.30 % Rotamer: Outliers : 0.28 % Allowed : 33.90 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.06 (0.29), residues: 366 loop : -1.33 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 54 TYR 0.020 0.001 TYR G 98 PHE 0.014 0.001 PHE E 43 TRP 0.010 0.002 TRP E 150 HIS 0.004 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 6633) covalent geometry : angle 0.79612 ( 8987) SS BOND : bond 0.00504 ( 8) SS BOND : angle 0.89397 ( 16) hydrogen bonds : bond 0.28861 ( 186) hydrogen bonds : angle 11.36225 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 ILE cc_start: 0.8790 (tp) cc_final: 0.8472 (mm) REVERT: E 49 VAL cc_start: 0.9275 (t) cc_final: 0.9034 (m) REVERT: E 168 ASP cc_start: 0.6886 (p0) cc_final: 0.6683 (p0) REVERT: G 129 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7556 (mm-30) outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 0.0952 time to fit residues: 16.2178 Evaluate side-chains 87 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.119596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.102890 restraints weight = 17545.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.102558 restraints weight = 12944.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.103596 restraints weight = 12637.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104045 restraints weight = 8953.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104424 restraints weight = 8889.181| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 6641 Z= 0.196 Angle : 0.695 7.771 9003 Z= 0.367 Chirality : 0.048 0.193 998 Planarity : 0.007 0.130 1167 Dihedral : 5.244 40.492 920 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.86 % Favored : 93.90 % Rotamer: Outliers : 6.98 % Allowed : 27.64 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.29), residues: 836 helix: None (None), residues: 0 sheet: -0.29 (0.27), residues: 385 loop : -1.31 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 54 TYR 0.029 0.002 TYR G 98 PHE 0.018 0.002 PHE G 99 TRP 0.011 0.002 TRP G 38 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 6633) covalent geometry : angle 0.69440 ( 8987) SS BOND : bond 0.00407 ( 8) SS BOND : angle 1.03077 ( 16) hydrogen bonds : bond 0.04179 ( 186) hydrogen bonds : angle 7.46762 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 95 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.5485 (tm-30) cc_final: 0.5259 (tm-30) REVERT: C 136 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6534 (mm-30) REVERT: C 213 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.5613 (t80) REVERT: G 105 TYR cc_start: 0.5233 (OUTLIER) cc_final: 0.4771 (p90) REVERT: G 129 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7502 (mm-30) REVERT: G 183 ASP cc_start: 0.8109 (t0) cc_final: 0.7887 (t0) REVERT: G 213 MET cc_start: 0.6936 (mtp) cc_final: 0.6727 (tpp) outliers start: 49 outliers final: 23 residues processed: 136 average time/residue: 0.0684 time to fit residues: 12.8271 Evaluate side-chains 103 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 128 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.118175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.101297 restraints weight = 17347.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.101117 restraints weight = 12202.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.102304 restraints weight = 11003.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.102514 restraints weight = 8445.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.102988 restraints weight = 8699.789| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6641 Z= 0.218 Angle : 0.692 11.425 9003 Z= 0.356 Chirality : 0.048 0.220 998 Planarity : 0.007 0.137 1167 Dihedral : 5.320 41.153 920 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 6.70 % Allowed : 26.78 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.29), residues: 836 helix: None (None), residues: 0 sheet: -0.28 (0.28), residues: 364 loop : -1.34 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 67 TYR 0.027 0.002 TYR G 98 PHE 0.017 0.002 PHE E 43 TRP 0.015 0.002 TRP G 38 HIS 0.003 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 6633) covalent geometry : angle 0.69100 ( 8987) SS BOND : bond 0.00410 ( 8) SS BOND : angle 1.13825 ( 16) hydrogen bonds : bond 0.03736 ( 186) hydrogen bonds : angle 7.08472 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 86 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: C 106 GLU cc_start: 0.5374 (tm-30) cc_final: 0.5157 (tm-30) REVERT: C 128 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6953 (m-80) REVERT: C 136 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6511 (mm-30) REVERT: E 204 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8173 (m) REVERT: G 105 TYR cc_start: 0.5386 (OUTLIER) cc_final: 0.5047 (p90) REVERT: G 129 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7697 (mm-30) REVERT: G 183 ASP cc_start: 0.8020 (t0) cc_final: 0.7751 (t0) outliers start: 47 outliers final: 34 residues processed: 124 average time/residue: 0.0679 time to fit residues: 11.7388 Evaluate side-chains 115 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 128 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 57 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 HIS ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.120963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104030 restraints weight = 17712.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.103523 restraints weight = 13040.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104674 restraints weight = 13459.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105192 restraints weight = 9229.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.106146 restraints weight = 8733.269| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6641 Z= 0.139 Angle : 0.622 11.895 9003 Z= 0.321 Chirality : 0.047 0.221 998 Planarity : 0.006 0.137 1167 Dihedral : 5.038 40.992 920 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 6.98 % Allowed : 26.50 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.29), residues: 836 helix: None (None), residues: 0 sheet: -0.22 (0.28), residues: 376 loop : -1.23 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 54 TYR 0.023 0.001 TYR G 98 PHE 0.016 0.002 PHE G 212 TRP 0.009 0.001 TRP G 38 HIS 0.004 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6633) covalent geometry : angle 0.62087 ( 8987) SS BOND : bond 0.00358 ( 8) SS BOND : angle 0.92173 ( 16) hydrogen bonds : bond 0.03068 ( 186) hydrogen bonds : angle 6.64249 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 85 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: C 106 GLU cc_start: 0.5512 (tm-30) cc_final: 0.5292 (tm-30) REVERT: C 128 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6885 (m-80) REVERT: C 136 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6459 (mm-30) REVERT: D 158 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6973 (mp) REVERT: E 204 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8200 (m) REVERT: G 105 TYR cc_start: 0.5386 (OUTLIER) cc_final: 0.5155 (p90) REVERT: G 129 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7736 (mm-30) REVERT: G 183 ASP cc_start: 0.7874 (t0) cc_final: 0.7660 (t0) outliers start: 49 outliers final: 29 residues processed: 127 average time/residue: 0.0781 time to fit residues: 13.3192 Evaluate side-chains 113 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 179 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 0.0060 chunk 61 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 HIS ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN G 128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.104961 restraints weight = 17711.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.104600 restraints weight = 12954.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.105486 restraints weight = 13930.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106097 restraints weight = 9552.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.106223 restraints weight = 9118.147| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6641 Z= 0.126 Angle : 0.614 11.446 9003 Z= 0.314 Chirality : 0.046 0.219 998 Planarity : 0.006 0.134 1167 Dihedral : 4.856 39.921 920 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.26 % Favored : 94.50 % Rotamer: Outliers : 6.27 % Allowed : 27.78 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.25 (0.27), residues: 395 loop : -1.04 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 77 TYR 0.020 0.001 TYR G 98 PHE 0.013 0.001 PHE E 39 TRP 0.006 0.001 TRP G 150 HIS 0.003 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6633) covalent geometry : angle 0.61322 ( 8987) SS BOND : bond 0.00346 ( 8) SS BOND : angle 0.79200 ( 16) hydrogen bonds : bond 0.02826 ( 186) hydrogen bonds : angle 6.27303 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: C 128 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: C 213 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5854 (t80) REVERT: D 158 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6984 (mp) REVERT: E 204 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8202 (m) REVERT: G 129 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7711 (mm-30) REVERT: G 183 ASP cc_start: 0.7840 (t0) cc_final: 0.7581 (t0) outliers start: 44 outliers final: 30 residues processed: 122 average time/residue: 0.0793 time to fit residues: 13.0950 Evaluate side-chains 113 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 128 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.119742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.102806 restraints weight = 17536.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.102802 restraints weight = 12352.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.103651 restraints weight = 13059.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104203 restraints weight = 8911.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.104361 restraints weight = 8377.110| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6641 Z= 0.161 Angle : 0.629 10.763 9003 Z= 0.322 Chirality : 0.046 0.222 998 Planarity : 0.006 0.131 1167 Dihedral : 4.891 40.731 920 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.86 % Favored : 93.90 % Rotamer: Outliers : 6.41 % Allowed : 27.49 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.23 (0.27), residues: 389 loop : -1.00 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.024 0.001 TYR G 98 PHE 0.015 0.002 PHE E 39 TRP 0.008 0.001 TRP G 150 HIS 0.004 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6633) covalent geometry : angle 0.62879 ( 8987) SS BOND : bond 0.00402 ( 8) SS BOND : angle 0.85789 ( 16) hydrogen bonds : bond 0.02902 ( 186) hydrogen bonds : angle 6.28647 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: C 136 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6432 (mm-30) REVERT: C 213 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5947 (t80) REVERT: D 158 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.7024 (mp) REVERT: E 204 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8250 (m) REVERT: G 129 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7818 (mm-30) REVERT: G 183 ASP cc_start: 0.7849 (t0) cc_final: 0.7629 (t0) outliers start: 45 outliers final: 35 residues processed: 117 average time/residue: 0.0712 time to fit residues: 11.6502 Evaluate side-chains 118 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 198 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.121249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104173 restraints weight = 17443.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.104042 restraints weight = 12812.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104985 restraints weight = 13496.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105500 restraints weight = 9209.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.106004 restraints weight = 8681.179| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6641 Z= 0.139 Angle : 0.618 10.677 9003 Z= 0.314 Chirality : 0.046 0.221 998 Planarity : 0.006 0.129 1167 Dihedral : 4.791 41.254 920 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.74 % Favored : 94.02 % Rotamer: Outliers : 5.56 % Allowed : 28.92 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.18 (0.27), residues: 389 loop : -0.97 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.022 0.001 TYR G 98 PHE 0.015 0.001 PHE E 39 TRP 0.007 0.001 TRP G 150 HIS 0.003 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6633) covalent geometry : angle 0.61795 ( 8987) SS BOND : bond 0.00371 ( 8) SS BOND : angle 0.78717 ( 16) hydrogen bonds : bond 0.02727 ( 186) hydrogen bonds : angle 6.11600 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: C 17 GLU cc_start: 0.6966 (pp20) cc_final: 0.6721 (pp20) REVERT: C 136 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6428 (mm-30) REVERT: D 158 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6970 (mp) REVERT: E 204 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8250 (m) REVERT: G 129 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7876 (mm-30) outliers start: 39 outliers final: 32 residues processed: 117 average time/residue: 0.0700 time to fit residues: 11.2974 Evaluate side-chains 115 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 179 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 43 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.122136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.105112 restraints weight = 17552.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104688 restraints weight = 13116.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.105643 restraints weight = 13085.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.106123 restraints weight = 9570.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.106486 restraints weight = 9455.382| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6641 Z= 0.116 Angle : 0.601 10.597 9003 Z= 0.307 Chirality : 0.046 0.219 998 Planarity : 0.006 0.128 1167 Dihedral : 4.754 41.254 920 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 5.27 % Allowed : 29.77 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.10 (0.27), residues: 387 loop : -0.93 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.019 0.001 TYR G 98 PHE 0.025 0.002 PHE G 212 TRP 0.006 0.001 TRP G 150 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6633) covalent geometry : angle 0.60092 ( 8987) SS BOND : bond 0.00350 ( 8) SS BOND : angle 0.71950 ( 16) hydrogen bonds : bond 0.02534 ( 186) hydrogen bonds : angle 5.95582 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: C 17 GLU cc_start: 0.6850 (pp20) cc_final: 0.6610 (pp20) REVERT: C 54 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.5467 (tmtt) REVERT: C 58 ASP cc_start: 0.2280 (OUTLIER) cc_final: 0.1238 (p0) REVERT: D 158 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6895 (mp) REVERT: E 168 ASP cc_start: 0.6877 (p0) cc_final: 0.6282 (p0) REVERT: E 204 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8229 (m) REVERT: G 129 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7629 (mm-30) outliers start: 37 outliers final: 29 residues processed: 121 average time/residue: 0.0808 time to fit residues: 13.1376 Evaluate side-chains 116 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 0.0970 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.120704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103723 restraints weight = 17725.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.103404 restraints weight = 12903.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104650 restraints weight = 11594.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104863 restraints weight = 8869.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105419 restraints weight = 9140.573| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6641 Z= 0.161 Angle : 0.658 10.070 9003 Z= 0.335 Chirality : 0.046 0.217 998 Planarity : 0.006 0.122 1167 Dihedral : 4.906 37.310 920 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.14 % Favored : 94.62 % Rotamer: Outliers : 5.70 % Allowed : 28.63 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.16 (0.28), residues: 372 loop : -1.05 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 187 TYR 0.023 0.002 TYR G 98 PHE 0.034 0.002 PHE G 212 TRP 0.011 0.002 TRP C 142 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6633) covalent geometry : angle 0.65804 ( 8987) SS BOND : bond 0.00384 ( 8) SS BOND : angle 0.83634 ( 16) hydrogen bonds : bond 0.02735 ( 186) hydrogen bonds : angle 6.12708 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: C 14 MET cc_start: 0.7935 (mtt) cc_final: 0.7706 (mtt) REVERT: C 17 GLU cc_start: 0.6775 (pp20) cc_final: 0.6518 (pp20) REVERT: C 54 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6210 (pttm) REVERT: C 58 ASP cc_start: 0.2407 (OUTLIER) cc_final: 0.1368 (p0) REVERT: C 136 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6500 (mm-30) REVERT: D 158 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6964 (mp) REVERT: E 168 ASP cc_start: 0.6903 (p0) cc_final: 0.6298 (p0) REVERT: E 204 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8250 (m) REVERT: G 129 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7622 (mm-30) outliers start: 40 outliers final: 33 residues processed: 114 average time/residue: 0.0737 time to fit residues: 11.5381 Evaluate side-chains 118 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 78 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.121147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.103974 restraints weight = 17604.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.103833 restraints weight = 13015.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104762 restraints weight = 13852.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.105301 restraints weight = 9498.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.105681 restraints weight = 8913.438| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6641 Z= 0.147 Angle : 0.649 9.015 9003 Z= 0.331 Chirality : 0.046 0.216 998 Planarity : 0.006 0.121 1167 Dihedral : 4.893 40.365 920 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.98 % Favored : 93.78 % Rotamer: Outliers : 5.84 % Allowed : 28.77 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.17 (0.28), residues: 372 loop : -1.03 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.022 0.001 TYR G 98 PHE 0.055 0.003 PHE D 26 TRP 0.007 0.001 TRP G 150 HIS 0.003 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6633) covalent geometry : angle 0.64843 ( 8987) SS BOND : bond 0.00375 ( 8) SS BOND : angle 0.78217 ( 16) hydrogen bonds : bond 0.02668 ( 186) hydrogen bonds : angle 6.07802 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: C 14 MET cc_start: 0.7940 (mtt) cc_final: 0.7712 (mtt) REVERT: C 17 GLU cc_start: 0.6735 (pp20) cc_final: 0.6483 (pp20) REVERT: C 54 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.6178 (pttm) REVERT: C 58 ASP cc_start: 0.2450 (OUTLIER) cc_final: 0.1383 (p0) REVERT: C 136 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6464 (mm-30) REVERT: D 158 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6946 (mp) REVERT: E 168 ASP cc_start: 0.6915 (p0) cc_final: 0.6456 (p0) REVERT: E 204 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8259 (m) REVERT: G 129 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7678 (mm-30) outliers start: 41 outliers final: 35 residues processed: 116 average time/residue: 0.0746 time to fit residues: 11.8058 Evaluate side-chains 118 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 208 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.121366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.104509 restraints weight = 17651.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104414 restraints weight = 12882.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105398 restraints weight = 13448.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.105885 restraints weight = 9240.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106238 restraints weight = 8781.667| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6641 Z= 0.141 Angle : 0.635 8.930 9003 Z= 0.323 Chirality : 0.046 0.214 998 Planarity : 0.006 0.121 1167 Dihedral : 4.856 40.625 920 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.98 % Favored : 93.78 % Rotamer: Outliers : 6.13 % Allowed : 28.63 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.23 (0.28), residues: 365 loop : -0.95 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.021 0.001 TYR G 98 PHE 0.025 0.002 PHE G 212 TRP 0.007 0.001 TRP G 150 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6633) covalent geometry : angle 0.63433 ( 8987) SS BOND : bond 0.00390 ( 8) SS BOND : angle 0.77478 ( 16) hydrogen bonds : bond 0.02638 ( 186) hydrogen bonds : angle 6.05125 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1252.16 seconds wall clock time: 22 minutes 22.13 seconds (1342.13 seconds total)